WO2010047835A2 - Double-stranded ribonucleic acids with rugged physico-chemical structure and highly specific biologic activity - Google Patents

Abstract

The invention relates to our discovery of a novel double-stranded ribonucleic acid (dsRNA) having specific biological activities, which includes acting as a selective agonist for activation of the Toll-like receptor 3. Its "rugged" molecular structure as measured by physico-chemical techniques is resistant to molecular unfolding (i.e., denaturation). This structure appears to be responsible for increased efficacy of dsRNA in therapeutic applications and improved biological activity (e.g., used as an immunoregulatory agent). Medicaments, processes for their manufacture, and methods for their use are provided herein.

Description

DOUBLE-STRANDED RIBONUCLEIC ACIDS WITH RUGGED PHYSICO- CHEMICAL STRUCTURE AND HIGHLY SPECIFIC BIOLOGIC ACTIVITY

CROSS REFERENCE TO RELATED APPLICATIONS This application claims priority benefit of U.S. provisional application,

Serial No. 61/193,030, filed October 23, 2008.

FIELD OF THE INVENTION

The invention relates to our discovery of a novel double-stranded ribo- nucleic acid (dsRNA) having specific biological activities, which includes acting as a selective agonist for activation of Toll-like receptor 3 (TLR3). Its "rugged" molecular structure as measured by physico-chemical techniques is resistant to molecular unfolding (i.e., denaturation). This structure appears to be responsible for increased efficacy of dsRNA in therapeutic applications and improved biological activity (e.g., used as an immunoregulatory agent).

BACKGROUND OF THE INVENTION

AMPLIGEN® (rintatolimod) poly(l):poly(Ci₂U) was developed as a synthetic double-stranded ribonucleic acid (dsRNA) for therapeutic applications based on an understanding of both the beneficial and adverse effects induced by poly(l):poly(C) on the physiology of a subject. Acting on the hypothesis that the nucleotide sequence requirements for beneficial and adverse effects are different, poly(l):poly(Ci₂U) was developed by us to preserve the beneficial aspects of dsRNA without the adverse effects of poly(l):poly(C) by modifying the latter's structure with the occasional introduction of uridylate into the poly(C) strand to produce duplexes containing specifically-configured regions which are not base paired (i.e., "mismatched") at the position of the modification. These regions accelerate dsRNA hydrolysis and lessen toxicity (Greene, 1984). On the other hand, the ability to induce interferon synthesis was retained as long as the modified dsRNA persisted for a half life of at least five minutes and the frequency of random insertion into the poly(ribocytidylic acid) strand was not greater than each 0.5 to 1.0 helical turn of perfectly base-paired dsRNA (Brodsky, 1987).

While poly(l):poly(C-ι₂U) is stable in solution, it is susceptible to hydrolysis like all other conventional nucleic acids. The hydrolysis is highly depen- dent on nucleic acid structure, as well as on the presence of nuclease and divalent cations, pH, and temperature. RNA is more susceptible to hydrolysis than DNA because of the 2'-OH group present in the former that facilitates hydrolysis. Moreover, poly(l):poly(Ci₂U) was designed to degrade more rapidly than other dsRNA in a nuclease-containing environment, such as blood and other tissue fluids. Nucleic acids are initially stable in physiological salt buffers at room temperature, but gradually begin to degrade with time. This hydrolysis rate is temperature dependent, increasing greatly at higher temperatures.

Properties of poly(l):poly(Ci₂U) are characterized by physico-chemical assays as shown in Table 1. Circular dichroism (CD) (e.g., ellipticity, melting behavior) is used to characterize the double-helical RNA structure, which is critical to potency. Briefly, Toll-like receptor 3 (TLR3) is activated by dsRNA (Alexopoulou, 2001 ), which leads to a host defense recruitment sequence, ultimately producing type I interferons (Schroeder, 2005). Initiation of interferon production by dsRNA binding to TLR3 requires RNA helical structure (Bell, 2006). Although X-ray diffraction and NMR alone are the definitive techniques to determine RNA second-order structure, CD measurement with a combination of scanning and thermal stress modes also can provide precise characterization of the critical double-helical structure. Indeed, minor changes in second- order structure of polynucleotides have been measured by CD (Gray, 1995), including the effects of ligand binding (Sumita, 2005).

TABLE 1. Biological Activity and Measured Attributes.

Measured Property Identity Attribute Activity Attribute

Conformation: Second Degree

CD: Ellipticity Double-Stranded RNA: binding to TLR3 integrity of helix

CD: Melting Behavior: Double-Stranded RNA: binding to TLR3

Melting Point V₂ Width integrity and uniformity of helix

Composition and Size

Maximum Size No. of Repeat Units Half Life: safety

C:U Ratio identity Half Life: safety

Therefore, circular dichroism can be employed to characterize the therapeutic potency of specifically-configured dsRNA including poly(l):poly(Ci₂U).

As regards adverse toxic effects, the half life of poly(l):poly(Ci₂U) was reduced to a safe level of about 4 to 5 minutes by precise substitution of the poly(C) strand, specifically the cytidine to uridine ratio (U.S. Patent 5,258,369). Introduction of the unpaired base uracil into the poly(C) strand at a ratio of 1 :12 (Greene, 1978) resulted in a minimum base-paired length of about one helical turn, which is required for the interaction of dsRNA with its bioactive receptor. Furthermore, placing a maximum size limitation of about 350 repeat units on the dsRNA resulted in a half life of about 4 to 5 minutes (Greene, 1978; Pitha, 1972).

It was our objective to identify a new family of improved dsRNA having specific physico-chemical structure and highly specific biological activities, which includes acting as a selective agonist for TLR3. Its rugged structure as measured by physico-chemical techniques is resistant to molecular unfolding (i.e., denaturation). Improvement in at least one or more biological activities may result from the rugged structure of this particular form of poly(l):poly(C-|₂U). Other advantages and improvements are described below, or would be appa- rent from the disclosure herein. SUMMARY OF THE INVENTION

It is an objective of the invention to provide improved forms of double- stranded ribonucleic acid (dsRNA). Their physico-chemical structure and biological activities are described herein. A "rugged" molecule resistant to unfolding (i.e., denaturation) of its helical structure has improved dsRNA activity as a selective agonist of Toll-like receptor 3 (TLR3). At least partial purification of rugged dsRNA from other dsRNA present after synthesis is expected to increase specificity in its use as a medicament and thereby reduce adverse effects attributable to the dsRNA that is not rugged. In one aspect, rugged dsRNA may be provided. Specifically-configured dsRNA may be of the general formula ribo(l_n) ^■ TJbO(C^gU)_n, ribo(l_n) ^• ribo(Cn. _I4U)_n, or ribo(ln) ^• ribo(Ci2U)_n, wherein the strands are comprised of ribonucleotides (ribo) and n is an integer from about 40 to about 40,000 repeats. For example, a strand comprised of poly(ribocytosinic4-₂₉uracilic acid), poly(ribo- cytosinicii-i₄uracilic acid), or poly(ribocytosinici₂uracilic acid) may be partially hybridized to an opposite strand comprised of poly(riboinosinic acid) such that the two strands form an RNA double helix that is not paired at the uracil base (i.e., mismatch).

After synthesis, rugged dsRNA may be isolated by at least subjecting the partially hybridized strands of a population of dsRNA to conditions that denature most dsRNA (at least 50 mol%, at least 80 mol%, at least 90 mol%, or at least 95 mol%) in the population, and then selection negatively or positively (or both) for dsRNA that remain partially hybridized. The purity of rugged dsRNA may thus be increased from less than about 0.1-10 mol% (e.g., less than about 5 mol%) relative to all RNA in the population after synthesis. It is preferred that the rugged dsRNA be more than about 80-98 mol% relative to all RNA present in the same mixture with the rugged dsRNA (at least 80 mol%, at least 90 mol%, at least 95 mol%, or at least 98 mol%) after selection. The denaturing conditions to unfold at least partially hybridized strands of dsRNA may comprise appropriate choice of buffer salts, pH, solvent, temperature, or any combination thereof. Conditions may be empirically determined by observation of the unfolding or melting of the duplex strands of ribonucleic acid. The yield of rugged dsRNA may be improved by partial hydrolysis of longer strands of ribonucleic acid, then selection of (partially) hybridized stands of appropriate size and resistance to denaturation.

The molecular weight of rugged dsRNA may be from about 250 Kda to about 320 Kda, or from about 270 Kda to about 300 Kda. Lengths of a single or both strands of rugged dsRNA may be from about 380 bases to about 450 bases, or from about 400 bases to about 430 bases. The number of helical turns made by duplexed RNA strands of rugged dsRNA may be from about 30 to about 38, or from about 32 to about 36. In another aspect, at least one or more different rugged dsRNA may be administered to a subject (e.g., human patient or animal) in need of such treatment. Rugged dsRNA may be administered at a dosage of from about 0.5 mg to about 60 mg/dose. This dosage may be administered once per week or month, or two or more doses per week or month. Each dose (e.g., from about 0.5 mg to about 60 mg, from about 5 mg to about 40 mg, or from about 10 mg to about 20 mg) may be provided to the subject without limitation to the formulation of the pharmaceutical composition, or its route of administration (although intravenous infusion is preferred). Use of an effective amount of rugged dsRNA to achieve a feeling of improved health and may be continued until at least one symptom is improved. The effective amount required to obtain such improvement may be identical to or higher than the amount required for maintenance of the effect(s).

The rugged dsRNA may act specifically through a TLR3 receptor. The function and phenotype of dendritic cells may be normalized in a subject (e.g., human patient or animal). Administering at least an effective amount of one or more rugged dsRNA to a subject (e.g., human patient or animal) may thereby decrease the number or reduce the severity of symptoms when the subject is afflicted by a disease or other pathological condition. Use of rugged dsRNA may correct dendritic cell maturation abnormalities in the subject without the hazard of inducing a cytokine storm.,

Antigen presenting cells (e.g., dendritic cells, macrophages, B cells) and mucosal tissues (e.g., gastric or respiratory epithelium) are preferred targets in the body for rugged dsRNA. One or more antigens may be presented to cells of the immune system, and the antigen(s) should be susceptible to the action of the rugged dsRNA acting selectively as a TLR3 agonist. Cells of the immune system, microbes, cancer cells, or other transformed cells may be susceptible to specific cytokine response patterns activated by rugged dsRNA acting selectively as a TLR3 agonist. The rugged dsRNA is preferably administered by intravenous infusion; intradermal, subcutaneous, or intramuscular injection; intranasal or intratracheal inhalation; or oropharyngeal or sublingual application. In another aspect, a medicament is provided as a pharmaceutical com- position. One or more different rugged dsRNA may be used for their beneficial effect(s) on a subject's health, as selective TLR3 agonist(s), to treat a disease or other pathological condition, or to manufacture medicaments or pharmaceutical compositions to treat a disease or other pathological condition. Optional inert ingredients of the composition include excipients and a vehicle (e.g., saline buffer or water) as a single dose or a multi-dose package (e.g., an injection vial or vials), and instructions for their use. Processes for making and using the pharmaceutical composition (medicament) are also provided. For example, one or more different rugged dsRNA may be formulated at a concentration from about 0.05 mg/mL to about 0.25 mg/mL (e.g., 10 mg dissolved in 4 ml_ or 20 mg dissolved in 8 ml_) in physiological phosphate-buffered saline and stored at from 2°C to 8°C in a refrigerator under aseptic conditions.

Further aspects of the invention will be apparent from our description of specific embodiments and the appended claims, and generalizations thereto.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 shows an HPLC chromatogram for poly(l):poly(Ci2U). The minor peak centered at a retention time of about 5.01 min is duplexed poly(l):poly(Ci₂U). The first major peak centered at a retention time of about 7.58 min is the single-stranded poly(Ci₂U). The second major peak centered at a retention time of about 10.05 min is the single-stranded poly(l). The molecular identity of each peak was determined by phbtodiode array (PDA) analysis. Figure 2 shows PDA analyses of the three HPLC peaks. Acetonitrile, which is used as a solvent, is responsible for absorbance at 230 nm. Absorbance at 245 nm indicates the presence of poly(l); absorbance at 265 nm indicates the presence of poly(Ci₂U). Fig. 2A is PDA analysis of the peak centered at a retention time of about 5.01 min, which contains poly(l) and poly(Ci2U). Fig. 2B is PDA analysis of the peak centered at a retention time of about 7.58 min, which contains poly(Ci₂U). Fig. 2C is PDA analysis of the peak i centered at a retention time of about 10.05 min, which contains poly(l).

Figure 3 shows size exclusion chromatography of complexes of TLR3- ECD and poly(l):poly(Ci₂U) (Fig. 3A)₁ the receptor TLR3-ECD only (Fig. 3B), and the ligand poly(l):poly(Ci₂U) only (Fig. 3C).

Figure 4 shows the effect of thermal stress (40⁰C) on the size of dsRNA as measured by analytical centrifugation. The decrease in sedimentation coefficient (S₂o,w) reflects a loss of size due to hydrolysis. Figure 5 shows the effect of thermal stress (40⁰C) on the size of dsRNA as measured by high performance liquid chromatography (HPLC). The rugged dsRNA peak increases as the larger poly(l) and poly(Ci₂U) strands hydrolyze.

DESCRIPTION OF SPECIFIC EMBODIMENTS Many uses of double-stranded ribonucleic acid (dsRNA) are known.

Efficacy of such treatments, which includes a decrease in the number and/or a reduction in the severity of adverse effects of nonselected populations of dsRNA, is improved by the use of at least partially purified, rugged dsRNA. The invention may be used to treat a subject (e.g., human or animal, especially birds, fishes, or mammals) with an incipient or established microbial infection, to treat a subject for other pathological conditions marked by abnormal cell proliferation (e.g., neoplasm or tumor), or for use as an immunostimulant to treat the subject for a disease or other pathological condition caused by at least infection, abnormal cell proliferation, chronic fatigue syndrome, or cell damage from autoimmunity or neurodegeneration. It is preferred that the amount of rugged dsRNA used is sufficient to bind Toll-Like Receptor 3 (TLR3) on immune cells of the subject. Innate or adaptive immunity may be triggered thereby. Preferably, rugged dsRNA may be used to activate TLR3 selectively without activating other Toll-like receptors like TLR4 or an RNA helicase like RIG-I or mda-5, or without inducing an excessive pro-inflammatory response as seen with the nonselective TLR3 agonist poly (l):poly(C) in a phenomenon known as "cytokine storm" in the art.

The subject may be infected with at least one or more bacteria, protozoa, or viruses. A pharmaceutical composition which is comprised of rugged dsRNA in an amount sufficient to bind to TLR3 is administered to the subject. Infection of the subject is reduced or eliminated thereby as assayed by decreased reco- very time, increased immunity (e.g., increase in antibody titer, lymphocyte proliferation, killing of infected cells, or natural killer cell activity), decreased division or growth of the microbe, or any combination thereof as compared to the subject not treated with the rugged dsRNA. The immunity induced by treatment is preferably specific for the microbe, although inducing innate immunity may also be efficacious.

An infection by a microbe may be treated. The microbe may infect a human or animal subject. The infection may be incipient or established. The microbe may be a bacterium, protozoan, or virus; especially those that cause disease (i.e., pathogenic microbes). Here, the terms "microbe" and "micro- organism" are used interchangeably.

The bacterium may be a species of the genus Bacillus (e.g., B. anthracis, B. cereus), Bartonella (B. henselae), Bordetella (e.g., B. pertussis), Borrelia (e.g., B. burgdorferi), Brucella (e.g., B. abortus), Campylobacter (e.g., C. jejuni), Chlamydia (e.g., C. pneumoniae), Clostridium (e.g., C. botulinum, C. difficile, C. perfringens, C. tetani), Corynbacterium (e.g., C. amycolatum, C. diphtheriae), Escherichia (e.g., E. coli O175:H7), Haemophilus (e.g., H. influenzae), Helio- bacter (e.g., H. pylori), Klebsiella (K. pneumoniae), Legionella (e.g., L. pneumophila), Listeria (e.g., L. monocytogenes), Mycobacterium (e.g., M. avium, M. bovis, M. branderi, M. leprae, M. tuberculosis), Mycoplasma (e.g., M. genita- Hum, M. pneumoniae), Neisseria (e.g., N. gonorrheae, N. meningitidis), Pneumocystis (e.g., P. carinii), Pseudomonas (P. aeruginosa), Rickettsia, (e.g., R. rickettsia, R. typhi), Salmonella (e.g., S. enterica), Shigella (e.g., S. dysente- riae), Staphylococcus (e.g., S. aureus, S. epidermidis), Streptococcus (e.g., S. pneumoniae, S. pyogenes), Treponema (e.g., T. pallidum), Vibrio (e.g., V. cholerae, V. vulnificus), or Yersinia (e.g., Y. pestis). These include Gram- negative or Gram-positive bacteria, chlamydia, spirochetes, mycobacteria, and mycoplasmas.

The protozoan may be a species of the genus Cryptosporidium (e.g., C. hominis, C. parvum), Entamoeba (e.g., E. histolytica), Giardia (e.g., G. intesti- nalis, G. lamblia), Leishmania (e.g., L. amazonensis, L. braziliensi, L. donovani, L. mexicana, L. tropica), Plasmodium (e.g., P. falciparum, P. vivax), Toxo- plasma (e.g., T. gondii), or Trypanosoma (e.g., T. bruci, T. cruzi).

The virus may be a DNA or RNA virus that infects humans and animals. DNA viruses include those belonging to the Adenoviridae, Iridoviridae, Papillo- maviridae, Polyomavirididae, and Poxviridae families (Group I double-stranded DNA viruses); the Parvoviridae family (Group Il single-stranded DNA viruses). RNA viruses include those belonging to the Birnaviridae and Reoviridae families (Group ill double-stranded RNA viruses); the Arteriviridae, Astroviridae, Caliciviridae, Hepeviridae, and Roniviridae families (Group IV positive single- stranded RNA viruses); and the Arenaviridae, Bornaviridae, Bunyaviridae, Filoviridae, Paramyxoviridae, and Rhabdoviridae families (Group V negative single-stranded RNA viruses). Rugged dsRNA may also be used to treat infection by DNA viruses from the Herpesviridae family and RNA viruses from the Flaviviridae, Hepadnaviridae, Orthomyxoviridae, Picornaviridae, Retroviridae, and Togaviridae families.

The subject may be afflicted by a disease or pathological condition that is characterized by abnormal cell proliferation (e.g., neoplasm or tumor, other transformed cells). A pharmaceutical composition which is comprised of rugged dsRNA in an amount sufficient to bind to TLR3 is administered to the subject. Disease, symptoms thereof, their number, or their severity in the subject may be reduced or eliminated thereby as assayed by improved morbidity or morta- lity, increased immunity (e.g., increase in antibody titer, lymphocyte proliferation, killing proliferating or transformed cells, or NK cell activity), decreased division or growth of proliferating or transformed cells, or any combination thereof as compared to the condition of a subject not treated with rugged dsRNA.

The subject's cells undergoing the abnormal proliferation may be a neoplasm or tumor (e.g., carcinoma, sarcoma, leukemia, lymphoma), especially cells transformed by a tumor virus (e.g., DNA or RNA virus carrying a trans- forming gene or oncogene) or otherwise infected by a virus associated with cancer. For example, Epstein-Barr virus is associated with nasopharyngeal cancer, Hodgkin's lymphoma, Burkitt's lymphoma, and other B lymphomas; human hepatitis B and C viruses (HBV and HCV) are associated with liver cancer; human herpesvirus 8 (HHV8) is associated with Kaposi's sarcoma; human papillomaviruses (e.g., HPV6, HPV11 , HPV16, HPV18, or combination thereof) are associated with cervical cancer, anal cancer, and genital warts; and human T-lymphotrophic virus (HTLV) is associated with T-cell leukemia and lymphoma. Cancers include those originating from the gastrointestinal (e.g., esophagus, colon, intestine, ileum, _' rectum, anus, liver, pancreas, stomach), genitourinary (e.g., bladder, kidney, prostate), musculoskeletal, nervous, pulmonary (e.g., lung), or reproductive (e.g., cervix, ovary, testicle) organ systems.

Dendritic cell maturation may be induced in the subject. Immature dendritic cells, which are capable of antigen uptake, may be induced to differentiate into more mature dendritic cells, which are capable of antigen presentation and priming an adaptive immune response (e.g., antigen-specific T cells). During their conversion from immature to mature dendritic cells, they may at least change cell-surface expression of major histocompatibility complex (MHC) molecules, costimulatory molecules, adhesion molecules, or chemokine receptors; decrease antigen uptake; increase secretion of chemokines, cytokines, or proteases; grow dendritic processes; reorganize their cytoskeleton; or any combination thereof. They may be induced to migrate to sites of inflammation or lymphoid tissue through blood or lymph to bring microbes, neoplastic or tumor cells, or other transformed cells into proximity. The subject may be vaccinated against at least infection or cancer. In some cases, e.g., virus-induced cancers, both infection and cancer may be treated. Immediately before, during, or immediately after vaccination (e.g., within 10 days of vaccination), a medicament or pharmaceutical composition which is comprised of rugged dsRNA in an amount sufficient to bind to TLR3 is administered to the subject. The immune response to a vaccine or dendritic cell preparation is stimulated thereby. The vaccine or dendritic cell preparation may be comprised of killed, fixed, or attenuated whole microbes or cells (e.g., proliferating or transformed); a lysate or purified fraction of microbes or cells (e.g., proliferating or transformed); one or more isolated microbial antigens (e.g., native, chemically synthesized, or recombinantly produced); or one or more isolated tumor antigens (e.g., native, chemically synthesized, or recombinantly produced). In situ vaccination may be accomplished by the subject's production of antigen at a site or circulation thereto (e.g., produced in a natural infection or cell growth, or shed antigen), and rugged dsRNA acting as an adjuvant thereon.

Specifically-configured dsRNA may be of the general formula ribo(l_n) ^• ribo(C-₄-2₉U)_n, ribo(ln) ^■ TJbO(C_11-I4U)_n, or ribo(!_n) ^■ ribo(C₁₂U)_n, wherein strands are comprised of ribonucleotides (ribo) and n is an integer from about 40 to about 40,000 repeats. For example, a poly(riboinosinic acid) strand may be partially hybridized to poly(ribocytosinic_4-29uracilic acid), poly(ribocytosinic_11-14 uracilic acid), or poly(ribocytosinic₁₂uracilic acid) strand such that the two strands do not form a duplex at the position of the uracil base (i.e., no base pairing at the mismatched position). Specifically-configured dsRNA include: ribo(l) ^• ribo(C₄, U), ribo(l) ^• NbO(C₁₁, U), ribo(l) ^■ ribo(C₁₃, U), ribo(l) ^• ribo(C₁₈, U), ribo(l) ^• ribo(C₂n, U)₁ ribo(l) ^• ribo(C₂4, G), and ribo(l) ^• ribo(C_29l G). Other specifically-configured dsRNA are based on copolynucleotides such as poly(CmU) and poly(C_mG) in which m is an integer from about 4 to about 29, or analogs of poly(riboinosinic acid) and poly(ribocytidilic acid) formed by modifying the ribo(ln) ^■ ribo(C_n) to incorporate unpaired bases (uracil or guanine) in the polyribocytidylate r(C_m) strand. Alternatively, specifically-configured dsRNA may be derived from ribo(l) ^• ribo(C) dsRNA by modifying the ribosyl backbone of poly(riboinosinic acid) ribo(l_n), e.g:_;, by including 2'-O-methyl ribosyl residues. Specifically-configured dsRNA may also be modified at the molecule's ends to add a hinge(s) to prevent slippage of the base pairs, thereby conferring a specific bioactivity in solvents or aqueous environments that exist in human biological fluids. The specifically-configured dsRNA described in U.S. Patents 4,024,222; 4,130,641 ; and 5,258,369 (incorporated by reference) are generally suitable for use according to the present invention after selection for rugged dsRNA. One or more different rugged dsRNA may be complexed with a stabili- zing polymer such as polylysine, polylysine plus carboxymethylcellulose, poly- arginine, polyarginine plus carboxymethylcellulose, or any combination thereof. Rugged dsRNA as at least a portion of a medicament or formulated with other compatible components in a pharmaceutical composition may be administered to a subject (e.g., human patient or animal, especially birds, fishes, or mammals) by any local or systemic route known in the art including enteral (e.g., oral, feeding tube, enema), topical (e.g., device such as a nebulizer for inhalation through the respiratory system, skin patch acting epicutaneously or transdermal^, suppository acting in the rectum or vagina), and parenteral (e.g., subcutaneous, intravenous, intramuscular, intradermal, or intraperitoneal injection; buccal, sublingual, or transmucosal; inhalation or instillation intra- nasally or intratracheally). The rugged dsRNA may be micronized by milling or grinding solid material, dissolved in a vehicle (e.g., sterile buffered saline or water) for injection or instillation (e.g., spray), topically applied, or encapsulated in a liposome or other carrier for targeted delivery. Dissolving the rugged dsRNA in water for injection (WFI) and injection of the composition into the subject are preferred. A carrier may be used to target the rugged dsRNA to the TLR3 receptor on antigen presenting cells and epithelium. For example, immature dendritic cells may be contacted in skin, mucosa, or lymphoid tissues. It will be appreciated that the preferred route may vary with the age, condition, gender, or health status of the subject; the nature of disease or other pathological condition, including the number and severity of symptoms; and the chosen active ingredient.

Formulations for administration (i.e., pharmaceutical compositions) may include aqueous solutions, syrups, elixirs, powders, granules, tablets, and capsules which typically contain conventional excipients such as binding agents, fillers, lubricants, disintegrants, wetting agents, suspending agents, emulsifying agents, preservatives, buffer salts, flavoring,, coloring, and/or sweetening agents. It will be appreciated that the preferred formulation may vary with the age, condition, gender, or health status of the subject; the nature of disease or other pathological condition, including the number and severity of symptoms; and the chosen active ingredient. The recommended dosage of rugged dsRNA will depend on the clinical status of the subject and the physician's or veterinarian's experience treating the disease or other pathological condition. Rugged dsRNA may be dosed at from about 0.5 mg to about 60 mg, from about 5 mg to about 40 mg, or from about 10 mg to about 20 mg in a subject (e.g., body mass of about 70-80 Kg for a human patient) on a schedule of once to thrice weekly (preferably twice weekly), albeit the dose amount and/or frequency may be varied by the physic- cian or veterinarian in response to the subject's symptoms. Nucleic acid in solid form may be dissolved in physiological phosphate-buffered saline and then infused intravenously. Cells or tissues that express TLR3 are preferred sites in the subject for delivering the nucleic acid, especially antigen presenting cells (e.g., dendritic cells, macrophages, B lymphocytes) and endothelium (e.g., endothelial cells of the respiratory and gastric systems). It will be appreciated that the preferred dosage may vary with the age, condition, gender, or health status of the subject; the nature of disease or other pathological condition, including the number and severity Of symptoms; and the chosen active ingredient. '

Dendritic cells which act as sentinel cells possess molecular surface structures that recognize pathogen-associated molecular patterns (PAMPs). These PAMPs include a set of Toll-like receptors (TLRs) that specifically recog- nize all dsRNA. In particular, dsRNA is a selective agonist of TLR3. Rugged dsRNA may be used as a selective agent for activation of TLR3. Dysfunction in co-stimulatory molecule (e.g., CD80, CD83, CD86) signaling in dendritic cells may be associated with the disease or other pathological condition to be treated. This abnormality may be normalized by using rugged dsRNA as a selective TLR3 agonist. The effects of rugged dsRNA may be inhibited or blocked by mutation of the TLR3 gene (e.g., deletion), down regulating its expression (e.g., siRNA), binding with a competitor for TLR3's ligand-binding site (e.g., neutralizing antibody) or a receptor antagonist, or interfering with a downstream component of the TLR3 signaling pathway (e.g., MyD88 or TRIF).

Circular dichroism (CD) is a physico-chemical technique for characterizing the conformation of specifically-configured dsRNA. It can also be used as a surrogate for binding of AMPLIGEN® (rintatolimod) poly(l):poly(C-i₂U) as a receptor agonist to its receptor TLR3. Furthermore, the helical structure of rugged dsRNA and the structural requirements for binding of specifically- configured dsRNA to TLR3 can be precisely characterized by CD.

Other physico-chemical techniques that may be used to characterize rugged dsRNA are reverse phase chromatography, PDA (photodiode array) analysis, gas pressure chromatography (GPC), specific ligand binding to TLR3 receptor, and sedimentation velocity measured by ultracentrifugation.

Rugged dsRNA provides a selective agent for dissecting out the effects of TLR3 activation on the immune system that was not previously available with such potency. Other agents like TLR adapters MyD88 and TRIF mediate signaling by all TLR or TLR3/TLR4, respectively. Thus, activation or inhibition of signaling through MyD88 or TRIF would not restrict the biological effects to those mediated by TLR3. Since the presence of TLR3 and its signaling is a requirement for AMPLIGEN® (rintatolimod) poly(l):poly(Ci₂U) to act as a receptor agonist, one could assay for the absence of TLR3 mutations, the presence of TLR3 protein, intact TLR3-mediated signaling, or any combination thereof in the cell or tissue of a subject prior to administration of the agonist. Such confirmation of TLR3 activity can be performed before, during, or after administration of the agonist. The agonist can be used to restrict the immune response to activation of TLR3 without activating other Toll-like receptors or RNA helicases. For example, abnormal cytokine (e.g., IFN-α, IFN-β, IFN-γ, TNF-α, IL-6, IL-10, IL-12) production or co-stimulatory molecule (e.g., CD80, CD83, CD86) signaling may have resulted from at least infection by the microbe, abnormal cell proliferation, autoimmune damage, or neurodegene- ration. This abnormality may be remodulated by using rugged dsRNA as a selective agonist of TLR3. Antigen presentation may be improved by conjugating the antigen (or a peptide analog thereof) to a ligand (or a receptor) that specifically binds to the cell surface (especially a component of the endosome- phagosome internalizing pathway) of one or more antigen presenting cells. The specific binding molecule may be an antibody to a cell surface molecule, or a derivative thereof (e.g., Fab, scFv). Expression of CD80, CD83, and CD86 may be analyzed by flow cytometry using fluorescently-labeled antibodies. Following overnight shipment, blood samples are stained within one hour of receipt. Conventional techniques are used for lysis of red blood cells and cell marker analyses by flow cytometry. Dendritic cells are identified based on low level expression of lymphocyte, monocyte, and NK cell markers along with high HLA-DR expression. Dendritic cells may also characterized according to CD11c and CD123 expression. Monocytes are identified by side scatter analysis and expression of a monocyte lineage marker. Analyses of CD80, CD83, and CD86 expression are performed after cell type identification. Measurements from healthy volunteers serve as controls, and they would indicate normal distribution and levels of marker expression for mature dendritic cells such as CD80, CD83, and CD86.

EXAMPLES

Synthesis of single-stranded poly(l) and poly(Ci₂U) began with enzy- matic polynucleotide synthesis of the polynucleotides from the respective mononucleotide starting materials: inosine for poly(l); cytidine (C) and uridine (U) for poly(C-i₂U). Then repetitive extraction and precipitation steps were used to remove residual impurities. The reaction solutions containing the products were concentrated by ultrafiltration and extracted with phenol four times. The concentrated and extracted solutio'ήs were precipitated, dissolved, and re- precipitated from aqueous ethanol (50:50). Whereas precipitated poly(l) was separated by centrifugation, the supernatant (waste) liquid phase of adherent PoIy(C-_I2U) was simply removed by aspiration. The precipitated pastes were re- dissolved, then concentrated, diafiltered, and further concentrated. The final bulk solutions containing polynucleotide was filtered. The filtered solution was freeze dried and the raw materials were stored frozen. Enzymatic Synthesis. The enzymatic synthesis used in the manufacturing process is dependent on the enzyme polynucleotide phosphorylase to synthesize polyinosinic acid and polycytidilic₁₂uridilic acid from their respective starting materials: cytidine 5'-diphosphate, trisodium salt (CDP Na₃), uridine 5'- diphosphate, disodium salt (UDP Na₂) and inosine 5'diphosphate, trisodium salt (IDP Na₃).

The enzyme catalyzes polynucleotide formation in a reversible reaction using Mg⁺⁺ as a co-factor and ATP as a source of energy. Polynucleotides were synthesized in the 5¹ to 3' direction with concurrent liberation of inorganic phosphate. Maximum yield was limited by the equilibrium between synthesis and reverse rates, degradative reaction (phosphorolysis). The progress of the reaction was followed by measuring the consumption of CDP or IDP. Viscosity of the reaction solution was also monitored. Purified water was filtered into the tank. The following ingredients were added to the tank one at a time with mixing: TRIS (hydroxymethyl) aminomethane, urea, magnesium chloride hexahydrate (MgCI GH₂O)₁ and ethylenediaminetetraacetic acid (edetate), disodium salt (EDTA Na₂). Raw material mononucleotides were also added.

Each ingredient was dissolved before the next one was added. After all of the ingredients were added, the solution was mixed for a minimum of 10 minutes. The mixture was then adjusted and purified water was added to obtain a final batch volume. This pre-enzyme reaction mixture was sampled for initial CDP or IDP concentration. The enzyme polynucleotide phosphorylase was added with mixing, whereupon the synthesis of polynucleotide commenced. Also, the viscosity profile at the optimal enzyme concentration must exhibit the usual increase in viscosity over time without significant decrease at the conclusion of the batch reaction; significant decrease in viscosity would indicate unde- sired degradation of polynucleotide. After the optimized amount of enzyme was added to the production batch, enzymatic synthesis progressed under constant, controlled agitation. The consumption of CDP or IDP was monitored approxi- mately every hour. The reaction was terminated by the addition of a stop solution. Viscosity was also monitored, for information only, during the process. Concentration of Reaction Solution. To minimize the required volume of phenol for extractions, the reaction product solution was concentrated.

Extraction of PoIy(I) and PoIy(Ci₂U). Residual enzyme was removed predominately by phenol extraction. The concentrated poly(Ci₂U) or poly(l) reaction product solutions was transferred into the extraction tank and 2M TRIS and sodium dodecyl sulfate (SDS) were added. After at least 5 minutes of mixing, liquefied phenol was added and the two phase solution was mixed to disperse the phenol phase in the aqueous phase. SDS was employed as a surface-active agent to facilitate dissolution of denatured protein into the phenol phase; TRIS was required to buffer the solution at an optimal pH for polynucleotide stability. The extraction mixture stands without mixing for pre-determined settling times to afford coalescence of the phases. The lower phenol waste phase is then pumped into containers for disposal. The location of the phenol cut was important in order to effectively separate phenol and protein from the upper, product phase, which contains poly(Ci2U) or poly(l). The phenol phase and an intermediate "rag" layer, which contains denatured protein solids, were discarded by visually observing the liquid flowing through the site glass at the tank outlet. When the phenol and rag layer disappeared and only product phase was observed, the outlet valve was closed and the phenol cut is consi- dered complete.

Precipitation of PoIy(Ci₂U) or PoIy(I). Contaminating phenol, SDS, and other salts remaining in solution were removed by precipitation with denatured ethyl alcohol. The poly(C₁₂U) or poly(l) concentrated solution was pumped into the precipitation tank. The denatured alcohol was added and after mixing the precipitate was separated.

Concentration and Diafiltration. Remaining bulk salts, a small amount of unreacted mononucleotide, and phenol were removed by diafiltration against water. The precipitate was dissolved in the original precipitation vessel with gentle mixing and heating. After dissolving, the solution was then concentrated and diafiltered against water for injection (WFI). The solution was filtered prior to freeze drying. Freeze Drying. The filtered poly(Ci₂U) or poly(l) material was loaded into a freeze drier. The material was frozen, and a vacuum was then applied. The product was considered dry when the programmed cycle was complete.

Manufacture of Poly(l):Poly(C₁₂U), Sterile Solution, for Intravenous Infusion. PoIy(I) and poly(Ci₂U) were dissolved in phosphate-buffered saline. Equal molar amounts were mixed in an annealing step, and cooled to room temperature. The solutions were sterile filtered.

Preparation of Buffer Vehicle, Excipient Solution. WFI was added to the tank. The excipients were added to the tank, and mixed. After mixing, the batch was sampled for pH and osmolality. Quality control must be within in-process limits prior to use for formulating the solutions containing poly(l) and poly(C-ι₂U).

Formulating PoIy(I) and PoIy(Ci₂U) solutions. An initial quantity of buffer solution was subdivided according to the batch formula and was filtered into the tank. PoIy(I) or PoIy(Ci₂U) was added to the buffer solution, and dissolved by mixing. The temperature of the solution was increased and maintained with mixing. The solution is then recirculated.

Annealing of Poly I : Poly C₁₂U Strands. Equivalent quantities of poly(l) and poly(C"i₂U) were transferred to the tank. With continual mixing, the temperature of the solution was increased. Samples were removed and tested for potency, and pH.

Sterile Filtration. The formulated bulk was sterile filtered in-line into a steam sterilized surge vessel.

Filling Operations. The filling operation was performed. After each vial was filled, a sterile stopper is used to stopper the vial. Stoppered vials were then conveyed from the aseptic processing area where they were sealed.

Rugged dsRNA was isolated from the annealed poly(l):poly(Ci₂U), which was prepared according to the above, by either analytical or preparative high performance liquid chromatography (HPLC) as a substantially purified and pharmaceutically-active molecule. Its molecular weight is about 286 Kda and is about 413 base pairs in length with about 34 complete turns of the RNA helix. It is only from about 1 mol% to about 4 mol% of an unfractionated AMPLIGEN® (rintatolimod) composition. Most dsRNA (about 96 mol% to about 99 mol%) after synthesis has a molecular weight of about 1.2 Mda and is about 2000 base pairs in length with about 166 complete turns of the RNA helix. The rugged dsRNA in the 5 min HPLC peak is about 4.9 times smaller than the bulk of the dsRNA, and more closely fits the ligand binding site of its cell surface receptor (TLR3).

Due to its structure, rugged dsRNA is unusually resistant to disruption of its RNA double helix and molecular unfolding. Thus, rugged dsRNA under the assay conditions described herein has about 100- to about 1 , 000-fold greater bioactivity than the same weight of unselected AMPLIGEN® (rintatolimod)

(a) Protection by PoIy(I)PoIy(Ci₂U) is by Selective Activation of TLR3

TLR3 Activation is Linked to Expression of IFN-α/β, IL-6, or IL-12. The relationship between IFN expression through TLR3 activation by dsRNA was established by Alexopoulou (2001 ) using 293T cells that express different Toll- like receptors (human TLR1 , TLR2, TLR3, TLR4, TLR5, TLR6, or TLR9). Only those cells containing human TLR3 showed marked expression of IFN-α/β, IL-6 or IL-12 when stimulated with poly (l):poly(C).

Poly(l):Poly(Ci₂U) Induces Host Defense Gene Modulation through Highly Selective Activation of TLR3. To understand the relationship of the TLR3-dependent innate immune response¹ to viral protection, Gowen (2007), subjected TLR3-deficient mice to dsRNA and measured expression of IFN-α/β, IL-6, and IL-12. The mice were also subsequently challenged by exposure to Punta Toro virus (PTV). Protection from the viral challenge was exquisitely sensitive to treatment with poly(l):poly(Ci₂U). Viral protection conferred by poly(l):poly(Ci₂U) was completely abolished for the case of TLR3-deficient mice. When contrasted to the partial but significant effectiveness of poly(l):poly(C) in TLR3^'A mice, it is clear that the structural substitutions of uridine in the cytidine strand of poly(l):poly(Ci₂U) are responsible for the highly specific, TLR3- dependent pathway. Furthermore, measurements of IFN-α/β and IL-6 directly link PTV protection or lack thereof to the modulation of these cytokines. This selective targeting of the TLR3 signaling pathway represents a significant advantage for therapeutic applications of poly(l):poly(Ci2U) as compared to other possible cytosolic mechanisms such as, for example, the use of unsubstituted dsRNA poly(l):poly(C) to stimulate cytokine production through RNA helicases such as MDA-5 and RIG-1 (Pichlmair, 2006).

(b) Binding of dsRNA to TLR3 Requires Helical Conformation of dsRNA

TLR3 Binding Site. Studying the structure of native TLR3 crystals, Choe (2005) found that TLR3 is a large horseshoe-shaped, right-handed, solenoid structure comprised of 23 leucine-rich repeats. The glycosylated, convex surface and negatively-charged concave surfaces are unlikely binding sites for dsRNA. Consequently, they proposed that dsRNA binding occurs at positively- charged patches located on the lateral face.

Using mutational analysis, Bell (2005, 2006) modified putative TLR3 binding sites in the positively-charged patches and observed formation of a dsRNA/TLR3 complex by size-exclusion chromatography. Despite the presence of numerous positively-charged residues, only two amino acids N541 and H539 were required for binding. The amido group of H539 could interact with dsRNA by hydrogen binding. Proximity of the second positively-charged residue N541 was also important, albeit the role of this amino acid was not as clear. Mutation to negatively-charged aspirate prevented binding by dsRNA, however conversion to a neutral alanine residue had no effect on binding by dsRNA.

Binding to TLR3 Requires Helical Conformation of dsRNA. Following the structural determination of most likely dsRNA binding surfaces on TLR3, Choe (2005) further proposed that the helical symmetry of dsRNA structure is necessary for the creation of the symmetric dimer form of activated, membrane- associated TLR3. In the ternary complex at the membrane surface, two symmetrically opposed TLR3 molecules are linked to either side of the helix of the common dsRNA.

As discussed above, using mutational analysis, Bell (2005, 2006) defined two highly conserved residues (N541 and H539) that are necessary for binding of dsRNA to TLR3. Moreover, the constraining requirement for ligand binding to both of these residues of TLR3 is satisfied only by the minor groove architecture of the (helical) conformation of dsRNA. When dsRNA phosphate binds in proximity to the charge sensitive H539, then the amide side (H541 ) becomes aligned with hydrogen bonding site of a 2' dsRNA hydroxyl only when helical dimensions are utilized.

(c) Helical Conformation of dsRNA and Alteration Thereto Accompanying Ligand Interactions are Precisely Characterized by Circular Dichroism Circular dichroism provides detailed information concerning the secondary, helical structures of dsRNA or alterations thereof which accompany ligand binding; as well as structural changes caused by enzymatic hydrolysis and addition of metal ions. Also, in the thermal stress mode, conformational information imparted by CD provides valuable insights to explain RNA stability. dsRNA Characterization. Gray (1995) showed that CD, applied in the mixing curve protocol, complemented ultraviolet absorption measurements to determine the stoichiometry of duplex RNA (A-G : C-T(U)). In this approach, the optical property is analyzed as a function of the added ratios of individual strands. The magnitudes of CD difference plots were maximal for 50:50 mixtures. Further, isodichroic behavior correlated with the formation of higher ordered or intra strand structures.

Ligand Interactions. Ghazaryan (2006) studied the ligand interaction of dsRNA with a family of positively charged pyridinium porphyrins. From CD measurements they found that minor modifications of porphyrin structure led to profound differences in mode of their iattachment to the double helical structure. Whereas TEtOHPyP4 associated by intercalation, TMetAIPyP4 attached by forming an external, self-stacking assembly.

Using circular dichroism, Brown (2002) showed that ADAR1 , a human dsRNA, (chimeric) converted from the A to Za form upon binding to adenosine deaminase. Corroboration was provided by crystallization of the complex and Raman spectroscopy. Sorrentino (2003) studied the powerful enzymatic degradation of dsRNA by human pancreateic ribonuclease (HP-RNase). Circular dichroism of the RNA/enzyme complex revealed that multi-site attachment of the dsRNA to HP-RNase was responsible for the destabilization of the RNA helix.

Stability of dsRNA. Studying the rRNA component of the 70S ribosomal complex, Sumita (2005) showed that psuedouridine substitutions stabilized the dsRNA helix based upon structural information provided by circular dichroism (CD). Specifically, pseudouridine substitutions created duplex regions with closing base pairs and water-mediated hydrogen bonds. Stabilization by Mg⁺⁺ was also characterized by CD in this study. Investigating the stability of RNA- DNA hybrids with variants in base composition, Lesnik (1995) showed that more stable hybrids retain ellipticity at 210 nm, a wavelength characteristic of the single component RNA band (A-form hybrid). In contrast, less stable hybrids showed lowered 210 nm ellipticity, values which were intermediate between the RNA and DNA components. A double-stranded RNA composition may be analyzed by high performance liquid chromatography (HPLC) as shown in Fig. 1. Analysis of a representative lot of AMPLIGEN® (rintatolimod) poly(l):poly(Ci₂U) resulted in two distinct peaks: one with retention times from 9.85 to 10.35 min corresponding to the poly(l) strand and from 7.30 to 7.80 min corresponding to the poly(Ci2U) strand. Rugged dsRNA is found at a retention time of about 5 min representing a molecular species uniquely resistant to denaturation and unfolding. Denatu- rating conditions would eliminate biological activity exclusively due to TLR3 receptor binding. This analytical method may also be used as a stability indicating assay and, in particular, it may be used to show that the rugged dsRNA is unusually resistant to disruption of its double helix and to molecular unfolding.

The identity of each peak is determined by analysis with a photodiode array (PDA) detector as shown in Fig. 2. At each selected retention time, a UV absorption scan of wavelengths from 200 nm to 360 nm was obtained. Duplex poly(l):poly(Ci₂U) and individual poly(l) and poly(d₂U) strands have their own specific peak absorption wavelengths. Absorption peaks centered at 248 nm and 265 nm indicate the presence of rugged dsRNA (about 286,000 daltons) having poly(l) and poly(Ci2U), respectively (Fig. 2A). Peak absorption centered at about 265 nm indicates the presence of the poly(C-ι₂U) strand (Fig. 2B). Peak absorption centered at about 248 nm indicates the presence of the poly(l) strand (Fig. 2C). Absorption centered at about 230 nm is due to acetonitrile used as solvent. Because of the relative scarcity of rugged dsRNA, the signal at 230 nm was subtracted from Fig. 2A.

Common name: poly(l) : poly(Ci₂U) predominant species

Chemical name: poly(inosinic acid):poly((cytidylic acid)i₂(uridylic acid))

CAS registry number: 3864-92-5

Other names: YY057

ht

Shown above are a partial view of poly(l):poly(Ci₂U) partially hybridized strands and the interaction of bases of individual poly(l) and the poly(Ci₂U) strands. Single inosine bases bind to cytosine bases, but not to the uridine base. In this structure, the poly (inosinic acid) is hydrogen bonded (dashed lines between bases) to poly (cytidylic acid), with uridylic acid substitution occurring on an average of every 12-13 bases.

Molecular formula: (13C₁₀H₁₁N₄O₇P)_n : ((12C₉H₁2N3θ7P)(C9H₁₁N2θ₈P))n Molecular size: about 1 ,200,000 daltons The number of repeat units (n) corresponding to the size of poly(l):poly(C₁₂U) of approximately 1.2 Mda is 2000 base pairs or 166 full helical turns. TABLE 2. Molecular Weight (MW) of Components.

MW Repeat Unit Repeat Unit MW lnosine 5' mono330 13 4527 phosphate

Cytidine 3' mono305 12 3880 phosphate

Uridylic acid 306 1 324

Overall Average: 318 N/A Sum: 8730

Common name: poly(l) : poly(C-i₂U) variant minor species (286,000 daltons) Chemical name: poly(inosinic acid):poly((cytidylic acid)i₂(uridylic acid))

ght

Shown above are a partial view of poly(l):poly(Ci₂U) partially hybridized strands and the interaction of bases of individual poly(l) and the poly(Ci₂U) strands. Single inosine bases bind to cytosine bases, but not to the uridine base. In this structure, the poly (inosinic acid) is hydrogen bonded (dashed lines between bases) to poly (cytidylic acid), with uridylic acid substitution occurring on an average of every 12-13 bases. This is "rugged" dsRNA. Molecular formula: (13C₁₀H₁₁N₄O₇P)_n : ((12C₉H₁2N3θ7P)(C9H₁₁N2θ₈P))n Molecular size: about 286,000 daltons The number of repeat units (n) corresponding to the size range of new variant, also termed rugged dsRNA (also termed peak 5 min on HPLC) is 286

Kda having 413 base pairs representing 34 complete turns of RNA helix and is resistant to disassembly of hydrogen-bonded strands under elevated thermal or abnormal ionic conditions.

Circular dichroism (CD) has been used to measure secondary structure (duplexed helices) of biological and synthetic polymers, including proteins and nucleic acids. CD is the measurement of absorption of right- or left-circular polarized light, at a specific wavelength, by chiral molecules. Chemical chirality is the property of a molecule being nonsuperimposable on its mirror image. An atom that makes its molecule chiral is called a chiral atom or, more commonly, a chiral center. Poly(l):poly(Ci₂U) has a number of chiral centers because of its primary and secondary structures. Chiral centers are found in the nucleotide bases, which form the two primary structures for the two individual RNA strands (ssRNA) of poly(l):poly(Ci₂U). Additional chiral centers come from hybridizing each ssRNA to the other through hydrogen bonding of their complementary bases. Hydrophobic bonding between adjacent bases of dsRNA is known as base stacking and produces a flexible, linear symmetrical, helical secondary structure of defined shape and size. CD spectra for AMPLIGEN® (rintatolimod) poly(l):poly(Ci₂U), which is dependent on the wavelength, are observed to be a function reflecting the Gaussian absorption for each chiral center. Therefore, the CD spectrum for a dsRNA such' as poly(l):poly(Ci₂U) is dependent on the complementary base pairing of double-stranded structures and the complex chirality of the resultant helical structure. It has been demonstrated by UV and CD spectroscopy that the biological activity of dsRNA is dependent on these specific spatial and steric configurations. Since perturbation of helical structure results in loss of the chiral centers characteristic of the secondary structure, the analysis and monitoring of secondary structure by CD provides a method to characterize the physico- chemical properties of poly(l):poly(Ci₂ll) that are associated with its bioactivity. The specific ellipticity measured in a wavelength scan provides a quantitative parameter, which is calculated as the ellipticity ratio at certain "critical" wavelengths. The value of this structural parameter, the ratio CD278/CD245. is unique to poly(l):poly(Ci2U). In a second CD analysis, ellipticity is measured during heating. As poly(l):poly(Ci₂U) is heated and thermally denatured, the individual poly(l) and poly(Ci₂U) strands unwind due to the breakdown of hydrogen bonding between complementary base pairs. When the temperature derivative of ellipticity is plotted, the minimum derivative value corresponds to melting temperature, defined as the point where 50% of the double-stranded conformation is unwound. The width at half-height of the peak, a measure of structural uniformity, also becomes an indication of its integrity. Taken together, these thermal indices provide a measure of the strength of the dsRNA helixes.

The wavelength scan detects two peaks: a first peak at 245 nm corresponding to the doubled stranded helix of the poly(l):poly(Ci₂U) and a second peak at 278 nm corresponding to the stacking of the nucleic acid's base pairs. Precision. AMPLIGEN® (rintatolimod) poly(l):poly(Ci₂U), lot 9807CD, at a concentration of 2.5 mg/mL was repeatedly assayed to investigate the precision of the CD assay. The percent relative standard deviations (%RSD) for the melting temperature (T_M), for the width at half-height for the first derivative of the melting curve and for the ratio of measurements of the CD peaks at 278 nm and 245 nm were calculated as 0.76%, 9.09%, and 1 .41 %, respectively. This demonstrated that CD assay of AMPLIGEN® (rintatolimod) poly(l):poly(Ci₂U) acts in a precise manner during thermal analysis for the determination of T_M and width at half height of the first derivative of the thermal melt curve and during the CD scan analysis for determination of the ratio of CD at 278 nm to CD at 245 nm. Specificity. This CD method for characterizing poly(l):poly(C₁₂U) is also specific because it can between differentiate duplexed nucleic acids and single- stranded nucleic acids, or other similar double-stranded nucleic acids that do not meet the manufacturing and release specifications for AMPLIGEN® (rintatolimod) poly(l):poly(Ci₂U). The specificity of this method, in regards to analysis of single versus double-stranded nucleic acids, was demonstrated by comparing scanning profiles and melting temperature curves. The scans of double-stranded molecules such as poly(l):poly(C-ι₂U), poly(l):poly(C), and poly(A):poly(U) differed significantly from those obtained during analysis of single-stranded molecules such as poly(l) and poly(Ci₂U). Furthermore, each of the CD scans was unique for the molecular species being assayed.

The specificity of the assay was also investigated to assess, unequivo- cally, the ability to detect compounds of closely related structure.

(a) Double-stranded ribonucleic acids of different nucleotide base composition, such as poly(l):poly(Ci₂U), poly(l):poly(C), and poly(A):poly(U).

(b) AMPLIGEN® (rintatolimod) poly(l):poly(C₁₂U) that meets the polymer size specification. (c) Double-stranded ribonucleic acid formulated from poly(l) and poly(C_xU_y) strands with a cytidine to uridine base ratio of 11-14 to 1 (C:U ratio = 11 :1 to 14:1 ).

The specificity of assays for dsRNA that differed in their nucleotide base composition was evidenced by comparison of CD scans and melting curves of similar, but different, double-stranded molecules, such as poly(l):poly(Ci₂U), poly(l):poly(C), and poly(A):poly(U). CD scanning profiles appear to be similar, as seen with the scans of AMPLIGEN® poly(l):poly(C-ι₂U) and poly(l):poly(C). But calculations of the ratios obtained at 278 nm and 245 nm, and subsequent t-test statistical analysis for equal means showed that the CD scan of AMPLI- GEN® (rintatolimod) differs significantly from similar dsRNA having different nucleotide base compositions. Specificity for the dsRNA of different nucleic acid base composition was also demonstrated by their thermal melting curves. Thermal melt curves for dsRNA differed significantly from each other. Statistical analysis (t-test for equal means) of data from the plots of the first derivative of the melting curves confirmed that the results obtained for their respective T_M and width at half-height are significantly different. Therefore, specificity of the CD method differentiates AMPLIGEN® (rintatolimod) from other dsRNA molecules by parameters of both the scan and the thermal melt profiles.

The CD method is specific for detection of poly(l):poly(Ci₂U) formulated from polymers not meeting the aforementioned specifications for size. When one or both polymers of the poly(l):poly(Ci₂U) molecule is outside the 4-8S size specification, the results from the CD analysis of these molecules do not meet specifications for AMPLIGEN® (rintatolimod) in regards to T_M and width at half- height of the first derivative of the thermal melt curve. The failure to meet specifications for these CD parameters is observed with these formulations even when the ± 1.5S size differential specification is satisfied. Relative to the data obtained from the thermal melt analyses of AMPLIGEN® (rintatolimod) formulations, the CD278/CD₂4₅ ratio determinations were less specific. CD scans alone did not differentiate between poly(l):poly(Ci₂U) and non-poly(l):poly(Ci₂U) formulations that did not meet manufacturing and/or release specifications for polymer size. As discussed above, the specificity of CD analysis is sensitive to the size of the single-stranded polymer strands. In addition, when the size difference between the complementary single-stranded polymer components, poly(l) and PoIy(Ci₂U), is 2.4S or greater, the CD thermal melt analyses will differentiate poly(l):poly(Ci₂U) from similar molecules not meeting the specification for the complementary polymer size differential.

CD analysis can distinguish between poly(l):poly(Ci₂U) and similar molecules that do not meet specifications for the amount of double strandedness or base pairing between the complementary poly(l) and poly(Ci₂U) strands. The amount of base pairing is dependent on the relative proportion of cytidylic acid to uridylic acid (C:U ratio) of the poly(C_xU_y) polymer. The ratio of cytidine to uridine in the poly(C_xU_y) polymer affects the melting temperature (T_M) as well as the width at half height of the first derivative of the melting curve. When the ratio of cytidine to uridine is less than 11 :1 , there is less double strandedness or base pairing (between polyinosinic acid and polycytidylic acid complemen- tary strands of the duplex RNA helix) than that for AMPLIGEN® (rintatolimod). This results in lower observed TM'S and larger widths at half-height for the first derivative of the thermal melt curves relative to those observed for poly(l): poly(C-ι₂U). Increasing the cytidine to uridine ratio of the poly(C_xU_y) strand increases the base pairing between the complementary strands of the helix and, therefore, increases the observed T_M and decreases the observed width at half- height of the first derivative of the thermal curve. The CD₂7β/CD₂₄5 ratio determi- nations were demonstrated to be less sensitive to differences in the C:U ratio in AMPLIGEN® (rintatolimod) formulations.

Both the size of the complementary polymer strands and the C: U ratio of the poly(Ci₂U) strand contribute to double strandedness of a poly(l):poly(Ci₂U ) molecule. The double strandedness, in turn, contributes to the efficacy of the drug product as discussed in the introduction. Therefore, CD method is an important analytical tool for characterization of poly(l):poly(C-ι₂U). Although CD scans and determinations of the CD₂₇₈/CD₂₄₅ ratio are less specific than the thermal melt analysis determinations of T_M and width at half-height of the first derivative of the melt curve, all three CD parameters may be used in combination for the thorough characterization and identification of poly(l):poly(C-i₂U).

Bioactivity and Stability of Rugged dsRNA

Bioactivity of dsRNA and poly(l):poly(C₁₂U) were measured, and then compared utilizing a ligand-binding assay. Stability was measured using the product release test, reverse phase HPLC assay.

A summary of the results is presented below, followed by more detailed discussion. The combination of enhanced bioactivity and much greater stability under the thermal stress of 40⁰C illustrate the "ruggedness" of this novel variant dsRNA (i.e., rugged dsRNA) and suggest that it will be more bioavailable than most of the dsRNA molecules in a formulation of Ampligen® (rintatolimod).

1. Bioactivity of rugged dsRNA shows two-fold greater binding affinity as compared to unselected dsRNA Rugged dsRNA binding sites become unsaturated at a ratio of 0.50:1 (TLR3 : rugged dsRNA) or higher. But binding sites for Ampligen® (rintatolimod) poly(l): PoIy(Ci₂U) become unsaturated at a ratio of 0.20:1 (TLR3 : unselected dsRNA) or higher.

2. Stability of rugged dsRNA is four-fold greater than unselected dsRNA Ampligen® (rintatolimod) poly(l): poly(Ci₂U) is stable (i.e., S_w,2o > 10.0) for less than 90 days when subjected to hydrolysis under thermal stress of 4O⁰C. By contrast, rugged dsRNA is stable for greater than 360 days under the same conditions.

3. Stability and bioactivity data show that rugged dsRNA is more bioavail- able than unselected dsRNA

From these stability and bioactivity considerations, rugged dsRNA is more bio- available for the relevant signaling receptor that conveys the therapeutic benefit. The rugged dsRNA has the additional benefit of maintaining long-term stability at ambient temperatures, which has important clinical implications for treating populations in regions of the world without adequate refrigeration capabilities.

Bioactivity Background

Toll-like receptors (TLR) are signaling molecules recognizing pathogen- associated molecular patterns (PAMP) and activating innate immune defense mechanisms. TLR3 recognizes dsRNA, the genomic structure of some viruses, and also an intermediate generated during viral RNA replication. dsRNA is also produced intracellular^ by stem-loop forming or with siRNA-aligned mRNAs. AMPLIGEN® (rintatolimod) is comprised of dsRNA molecules that act through TLR3 binding and downstream signaling events. While poly(l):poly(C) signaling has alternate routes, the poly(l):poly(Ci₂U) pathway acts exclusively through TLR3 binding as AMPLIGEN® (rintatolimod) treatment protects TLR3^+/+ but not TLR3^'7' mice from Punta Toro virus infection. TLR3^"'^' cells do not produce IFN upon poly(l):poly(Ci₂U) treatment while IFN is induced by poly (l):poly(C) in TLR3 knockout cells. The TLR3 molecule ectodomain (ECD) conformation and its relation to binding of dsRNA is well characterized, including the prospective binding site. Amino acids H539 and N541 are involved in the interaction with the double helix. Mutational analysis of these amino acids at the binding site further strengthens the argument. The effect of length and structure of dsRNA on TLR3 binding and IFN induction is known. lnosine₃₀ (ho):poly(C) or poly(l):Cytosine₃₀ (C₃o) induced interferon (IFN), but shorter dsRNA stretches do not induce IFN. Compared to them, however, IFN induction by poly(l):poly(C) was always superior. l₂o:C_2O, l₃o:C-₃o. and

were ineffective IFN inducers. Therefore, characterizing AMPLIGEN® (rintatolimod) by its TLR3 binding capacity is a biomarker to predict its biological activity.

Bioactivity Method

A range of ratios of TLR3-ECD to unselected Ampligen® (rintatolimod) or rugged dsRNA are reacted by the method of Leonard (2008). The components are separated by the size-exclusion chromatographic method described below. From the peak quantities of free TLR3-ECD and the ligand- receptor complex, the ratio of TLR3-ECD that is required for saturation of either Ampligen® (rintatolimod) or rugged dsRNA is determined. This threshold TLR3- ECD/dsRNA ratio provides a direct indication of the strength of the ligand- receptor binding and, therefore, of bioactivity. The following method is an adaptation of the experimental procedures used to characterize TLR3 ligand binding at a molecular level. Since TLR3- ECD (1.12 x 10² Kda) and poly(l):poly(C₁₂U) (0.2-2 x 10³ Kda) have different elution patterns, they can be separated from each other by size-exclusion chromatography (SEC). According to results obtained from poly(l):poly(C) using a SUPERDEX 200 PC 3.2/30 column and collecting 80μl fractions, most of the poly(l):poly(C) appears in fractions 3-5 while TLR3-ECD is eluted in fractions 9- 12 (Bell, 2005).

The binding of TLR3-ECD to poly(l):poly(C) or poly(l):poly(Ci₂U) creates a complex that is larger in size than either of the initial components. The later eluting free TLR3-ECD is separated from the complex. Optimization of the separation identified that the SUPEROSE 200 PC column afforded superior binding by reducing tailing, due to absence of nonspecific interactions with dsRNA.

Fig. 3 shows the resulting chromatograms obtained from the reacted mixture of TLR3-ECD / poly(l):poly(Ci₂U) compared to component injections of TLR3-ECD and poly(l):poly(C-ι₂U) alone, respectively. Characterization of Peaks. Identification and quantitation of TLR3-ECD in size-exclusion chromatography fractions is possible in an ELISA format. The commercially-available TLR3-ECD is a His tag-containing recombinant protein. A capture anti-His tag antibody immobilizes TLR3-ECD in a microplate well. A second, biotinylated primary antibody quantitatively binds to the immobilized TLR3-ECD. This secondary antibody is selected to have an epitope distal from the dsRNA binding site on the TLR3-ECD molecule and also from the epitope recognized by the capture antibody. HRP-conjugated streptavidin recognizes the biotinylated second primary antibody. The appropriate substrate metabo- lized by HRP produces a soluble color suitable for quantitative measurement of TLR3-ECD.

AMPLIGEN® (rintatolimod) concentration in the size-exclusion chromatography fractions is measured by fluorescence using standard dilutions and chromatography fractions in a quantitative riboGreen test. This assay permits testing of AMPLIGEN® (rintatolimod) out-of-the-bottle (i.e., not selected for rugged dsRNA) without further processing, preparation, or extraction, thereby maintaining its condition as a pharmaceutical.

Bioactivity Results. Results in Table 3 show the percentage of free TLR3-ECD that remains in a series of reactions using different ratios of TLR3- ECD to dsRNA. These studies were conducted with either unselected AMPLIGEN® (rintatolimod) as well as rugged dsRNA.

Binding of TLR3-ECD to rugged dsRNA is more effective than binding of TLR3-ECD to unselected AMPLIGEN® (rintatolimod). An approximately 2-fold greater ratio of TLR3-ECD is required to "unsaturate" rugged dsRNA (- 0.50:1 ) as compared to AMPLIGEN® (rintatolimod) (0.25 : 1 ). Also, the binding profile at various ratios shows a much sharper endpoint for saturation for the case of rugged dsRNA which may reflect greater structural uniformity for this more compact dsRNA. Table 3. Bioactivity Measurements of Unselected vs. Rugged dsRNA.

The TLR3 binding of rugged dsRNA is 2-fold better than receptor binding of unselected AMPLIGEN® (rintatolimod). Free TLR3 (area >10%) appears at a TLR3 : dsRNA ratio of 0.25:1 for unselected AMPLIGEN® (rintatolimod) as compared to a 0.50:1 for rugged dsRNA

Stability of Rugged dsRNA. Stability of poly(l):poly(C₁₂U) was measured at an accelerated temperature condition of 4O⁰C as compared to the long-term storage temperature of from 2°C to 8°C. As shown in Fig. 5, the size of poly(l): poly(Ci₂U) decays at this temperature as measured by analytical ultracentrifu- gation (S₂o,w). Decrease in size is due to unfolding of the double helix (loss of hydrogen bonds) and concurrent hydrolysis of the phosphodiester bonds. The bioactivity of dsRNA requires a sedimentation coefficient from about 10.0 to about 15.0 S(2o,w), whereas the size of poly(l):poly(Ci2U) at more than 180 days indicates a loss of bioactivity at about 8.0 S(₂o,w)-

Fig. 6 shows the results of a second stability indicating parameter, the reversed phase HPLC assay, previously described, that separates poly(l): poly(Ci₂U) into its individual strands. It is clearly evident that hydrolysis begins with the poly(l) strand followed by the PoIy(Ci₂U) strand. HPLC results show that loss of size does not begin until commencement of the hydrolysis of the second strand poly(Ci₂U); the RNA molecule retains double-stranded structure when only one of the strands undergoes hydrolysis. This loss of size at about 90 days occurs with the hydrolysis of both poly(l) and poly(C-ι₂U) strands.

Importantly, the rugged dsRNA (5 min) peak is entirely unaffected by thermal stress. In fact, it increases in relation to the poly(l) and poly(Ci2U) strands. This conclusively shows that rugged dsRNA is not only "rugged" but can form spontaneously from smaller strands of degraded poly(l):poly(Ci2U).

Patents, patent applications, books, and other publications cited herein are incorporated by reference in their entirety. In stating a numerical range, it should be understood that all values within the range are also described (e.g., one to ten also includes every integer value between one and ten as well as all intermediate ranges such as two to ten, one to five, and three to eight). The term "about" may refer to the statistical uncertainty associated with a measurement or the variability in a numerical quantity which a person skilled in the art would understand does not affect operation of the invention or its patentability.

All modifications and substitutions that come within the meaning of the claims and the range of their legal equivalents are to be embraced within their scope. A claim which recites "comprising" allows the inclusion of other ele- ments to be within the scope of the claim; the invention is also described by such claims reciting the transitional phrases "consisting essentially of (i.e., allowing the inclusion of other elements to be within the scope of the claim if they do not materially affect operation of the invention) or "consisting of (i.e., allowing only the elements listed in the claim other than impurities or inconse- quential activities which are ordinarily associated with the invention) instead of the "comprising" term. Any of these three transitions can be used to claim the invention.

It should be understood that an element described in this specification should not be construed as a limitation of the claimed invention unless it is explicitly recited in the claims. Thus, the granted claims are the basis for determining the scope of legal protection instead¹ of a limitation from the specification which is read into the claims. In contradistinction, the prior art is explicitly excluded from the invention to the extent of specific embodiments that would anticipate the claimed invention or destroy novelty.

Moreover, no particular relationship between or among limitations of a claim is intended unless such relationship is explicitly recited in the claim (e.g., the arrange-ment of components in a product claim or order of steps in a method claim is not a limitation of the claim unless explicitly stated to be so). All possible combinations and permutations of individual elements disclosed herein are considered to be aspects of the invention. Similarly, generalizations of the invention's description are considered to be part of the invention. From the foregoing, it would be apparent to a person of skill in this art that the invention can be embodied in other specific forms without departing from its spirit or essential characteristics. The described embodiments should be considered only as illustrative, not restrictive, because the scope of the legal protection provided for the invention will be indicated by the appended claims rather than by this specification.

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Claims

WHAT IS CLAIMED IS:

1. An isolated double-stranded ribonucleic acid (dsRNA) which is resistant to denaturation under conditions that are able to separate hybridized poly(riboinosinic acid) and poly(ribocytosinic acid) strands.

2. The dsRNA of Claim 1 which contains only partially hybridized strands.

3. The dsRNA of Claim 1 , wherein only a single strand of said dsRNA comprises one or more uracil or guanine bases that are not based paired to an opposite strand.

4. The dsRNA of Claim 3, wherein said single strand is partially hybridized to an opposite strand comprised of poly(riboinosinic acid).

5. The dsRNA of Claim 3, wherein said single strand is comprised of poly (ribocytosinic_4-29uracilic acid).

6. The dsRNA of Claim 5, wherein said single strand is partially hybridized to an opposite strand comprised of poly(riboinosinic acid).

7. The dsRNA of Claim 1 , wherein both strands of said dsRNA comprise one or more uracil or guanine bases that are not based paired to an opposite strand.

8. The dsRNA of Claim 1 , wherein a strand of said dsRNA is comprised of ribo(ln) ^• ribo(C4-29U)_n, in which ribo is a ribonucleotide and n is an integer from 40 to 40,000.

9. The dsRNA of Claim 8, wherein a strand of said dsRNA is comprised of ribo(ln) ^■ TiDo(C-Ii-I₄U)_n, in which ribo is a ribonucleotide and n is an integer from 40 to 40,000.

10. The dsRNA of Claim 9, wherein a strand of said dsRNA is comprised of ribo(ln) ^• ribo(Ci₂U)_n, in which ribo is a ribonucleotide and n is an integer from 40 to 40,000.

11. The dsRNA of any one of Claims 1 -10 which has a molecular weight from about 250 Kda to about 320 Kda.

12. The dsRNA of any one of Claims 1-10 which has at least one strand of a length from about 380 bases to about 450 bases.

13. The dsRNA of any one of Claims 1-10 which has from about 30 to about 38 helical turns of duplexed RNA strands.

14. A composition comprising one or more different dsRNA as defined in Claim 1.

15. Use of dsRNA as defined in any one of Claims 1 to 14 to manufacture a medicament or pharmaceutical composition.

16. A method of treating a subject, said method comprising administration to the subject of at least the dsRNA defined in any one of Claims 1 to 14 or at least the composition of Claim 15 in a therapeutic amount.

17. The method according to Claim 16, wherein the therapeutic amount of at least said dsRNA or said composition is infused intravenously.

18. The method according to Claim 16, wherein the therapeutic amount is injected intradermal^, subcutaneously, or intramuscularly; inhaled intranasally or intratracheal^; or applied intranasally, intratracheally, oropharyngeally, or sublingually.